Abstract 81: In depth single cell profiling of a case of breast cancer bone metastases with associated organoid models reveal a precision medicine approach to treatment
Authors: Kai Ding, Fangyuan Chen, Nolan Priedigkeit, Daniel D. Brown, Tanya Heim, Rebecca Watters, Kurt Weiss, Peter C. Lucas, Jennifer M. Atkinson, Steffi Oesterreich, Adrian V. Lee
Journal: Cancer Research (2022)

Abstract Occurring in 65-80% of metastatic breast cancer (BC), bone metastasis (BoM) is the major cause of BC related mortality. Lack of understanding of BoM evolution and heterogeneity at patient specific levels and precise application of targeted therapies are major challenges of managing BoM. In this study, we described in depth histologic and molecular characterization of a case of invasive lobular breast cancer (ILC) bilateral metastasis to bone, and identified and tested potential targets for treating BoM. H&amp;E/IHC staining, whole exome sequencing (WES), and RNAseq were performed on FFPE primary tumor and pelvis and tibia BoMs collected from our study case. Organoids were derived from the two BoMs and single cell RNA sequencing (scRNAseq) undertaken on the organoids and their originating tumors. H&amp;E/IHC demonstrated evolution of the disease from an ER+ primary ILC to ER- BoM with mixed lobular and ductal carcinoma features. WES revealed two druggable mutations including PIK3CA (E545K) and BRCA1 (D1813H/H399P). RNAseq revealed upregulation of TGF-β, Wnt/beta-catenin and PI3K pathways, epithelial to mesenchymal transition (EMT) and angiogenesis in BoM compared to primary tumor, representing promising targets for BoM. scRNAseq revealed 5 major cell types including epithelial, fibroblasts, immune, osteoclasts and endothelial cells, and pronounced intracellular heterogeneity. Six epithelial clusters were identified, featuring high TNF-α signaling, high partial EMT signatures regulated by PRRX1/2, TWIST1/2, and FOXS1, high proliferation, and endocrine resistance signatures. In fibroblasts, 9 clusters were identified representing ECM remodeling, angiogenesis, osteoclast-like, MSC, IFN response and myofibroblasts. Immune cells majorly composed of monocytes/macrophages, CD4+, CD8+ and Treg T cells, and NK cell. WES and scRNAseq analysis demonstrated that organoids preserved mutational landscape and cellular heterogeneity of matched BoMs. Consistent with the BRCA1 and PIK3CA mutations, organoids were responsive to a PARP (Talazoparib: IC50 1.3uM) and PI3K (Alpelisib: IC50 4-9uM) inhibitors. In summary, we have identified potential therapeutic targets from understanding evolution and heterogeneity of BC BoM, and evaluated these in patient-specific organoids, thereby providing insights for the design of a precision medicine based clinical treatment strategy. Citation Format: Kai Ding, Fangyuan Chen, Nolan Priedigkeit, Daniel D. Brown, Tanya Heim, Rebecca Watters, Kurt Weiss, Peter C. Lucas, Jennifer M. Atkinson, Steffi Oesterreich, Adrian V. Lee. In depth single cell profiling of a case of breast cancer bone metastases with associated organoid models reveal a precision medicine approach to treatment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 81.